Background

Mucosa-associated bacteria are believed to play a more prominent role in the pathogenesis of Crohn's disease (CD) as they are in closer contact to the gut immune system. Our aim was to study temporal changes of the microbiota in CD patients undergoing ileocecal resection and to identify the predictive value of recurrence-related microbiota.

Methods

A total of 204 samples from CD patients undergoing ileocecal resection were prospectively collected: biopsies were taken from the resected intestine (histologically inflamed (N=63) and non-inflamed ileum (N=56)) and from the neoterminal ileum (N=85) during postoperative endoscopy at month 6. Postoperative endoscopic recurrence (POR) was defined by a Rutgeerts score ≥i2b. The microbiota was evaluated by 16S rDNA sequencing using an Illumina MiSeq platform. Calculation of alpha and beta diversity and statistical analysis were performed in QIIME.

Results

At the time of surgery, the inflamed mucosa had a lower abundance of Actinomyces (FDR=0.05) compared to the non-inflamed mucosa.

Six months after resection, alpha diversity increased significantly compared to baseline samples in patients with recurrence (p=0.011) but not in patients without recurrence. An enrichment in Lachnospiraceae was observed in all patients at month 6 when compared to baseline samples (FDR<0.001). In recurrence patients, also Fusobacteriaceae (FDR=0.002) and Halomonadaceae (FDR=0.07) increased significantly after surgery when compared to baseline. Patients without recurrence on the other hand showed a decrease of Peptostreptococcaceae (FDR=0.08).

At month 6, patients with POR had a higher abundance of taxa belonging to Negativicutes (FDR=0.04) and Fusobacteria (FDR=0.04) compared to the remission patients.

A small subset of CD patients was on antibiotics at the time of surgery. Alpha diversity of the inflamed and non-inflamed mucosal microbiota was significantly reduced in antibiotics users (N=6 and 7; p=0.004 and 0.009 respectively). A strong impact was seen on many taxa including a reduction of Clostridia, Bacteroidaceae and increase of Flavobacteria and Bacilli.

Conclusion

At the time of resection, differences in microbiome composition between inflamed and non-inflamed mucosa are limited. The impact of ileocecal resection on the mucosal microbiome is defined by an increase of Lachnospiraceae. Recolonization after resection in patients developing POR differs from patients without recurrence by an increase of members belonging to Fusobacteriaceae and Halomonadaceae families. Postoperatively, the increased levels of Fusobacteria and Negativicutes (Veillonellaceae), which previously have been associated with inflammation in pediatric patients with new onset of CD, may be involved in the development of early POR.